Crppa (CDP-L-ribitol pyrophosphorylase A) - Rat Genome Database
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Gene: Crppa (CDP-L-ribitol pyrophosphorylase A) Rattus norvegicus
Analyze
Symbol: Crppa
Name: CDP-L-ribitol pyrophosphorylase A
RGD ID: 1359368
Description: Predicted to have D-ribitol-5-phosphate cytidylyltransferase activity and protein homodimerization activity. Predicted to be involved in axon guidance and protein O-linked mannosylation. Predicted to localize to cytosol. Human ortholog(s) of this gene implicated in autosomal recessive limb-girdle muscular dystrophy type 2U and congenital muscular dystrophy-dystroglycanopathy A7. Orthologous to human CRPPA (CDP-L-ribitol pyrophosphorylase A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cisplatin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase-like protein; D-ribitol-5-phosphate cytidylyltransferase; isoprenoid synthase domain containing; isoprenoid synthase domain-containing protein; Ispd; LOC493574; Nip; notch1-induced protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2653,120,264 - 53,397,030 (+)NCBI
Rnor_6.0 Ensembl655,881,387 - 56,159,464 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0655,880,136 - 56,159,466 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0665,490,939 - 65,818,620 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4655,139,155 - 55,419,630 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1655,421,454 - 55,422,754 (+)NCBI
Celera652,259,290 - 52,534,570 (+)NCBICelera
Cytogenetic Map6q16-q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IBA,IEA,ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:22522420   PMID:22522421   PMID:23217742   PMID:26687144  


Genomics

Comparative Map Data
Crppa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2653,120,264 - 53,397,030 (+)NCBI
Rnor_6.0 Ensembl655,881,387 - 56,159,464 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0655,880,136 - 56,159,466 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0665,490,939 - 65,818,620 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4655,139,155 - 55,419,630 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1655,421,454 - 55,422,754 (+)NCBI
Celera652,259,290 - 52,534,570 (+)NCBICelera
Cytogenetic Map6q16-q21NCBI
CRPPA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl716,087,525 - 16,421,538 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl716,087,525 - 16,502,504 (-)EnsemblGRCh38hg38GRCh38
GRCh38716,087,525 - 16,421,538 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37716,127,150 - 16,461,163 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36716,097,786 - 16,427,472 (-)NCBINCBI36hg18NCBI36
Celera716,106,872 - 16,440,699 (-)NCBI
Cytogenetic Map7p21.2NCBI
HuRef716,012,324 - 16,347,484 (-)NCBIHuRef
CHM1_1716,126,841 - 16,460,716 (-)NCBICHM1_1
CRA_TCAGchr7v2716,180,240 - 16,514,081 (-)NCBI
Crppa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391236,430,334 - 36,739,502 (+)NCBIGRCm39mm39
GRCm39 Ensembl1236,431,449 - 36,739,502 (+)Ensembl
GRCm381236,380,575 - 36,689,503 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1236,381,450 - 36,689,503 (+)EnsemblGRCm38mm10GRCm38
MGSCv371237,108,106 - 37,416,031 (+)NCBIGRCm37mm9NCBIm37
MGSCv361236,891,849 - 37,015,131 (+)NCBImm8
Celera1237,825,234 - 38,127,522 (+)NCBICelera
Cytogenetic Map12A3NCBI
Crppa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541019,359,868 - 19,614,344 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541019,359,495 - 19,614,283 (-)NCBIChiLan1.0ChiLan1.0
CRPPA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1716,076,235 - 16,405,268 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl716,077,091 - 16,405,220 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0716,747,569 - 17,078,389 (-)NCBIMhudiblu_PPA_v0panPan3
CRPPA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1430,648,128 - 30,989,604 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11430,697,060 - 30,989,423 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Crppa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365462,658,195 - 2,945,542 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CRPPA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl985,415,550 - 85,710,752 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1985,419,401 - 85,711,146 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2994,460,506 - 94,549,186 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CRPPA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12141,691,771 - 42,008,484 (+)NCBI
ChlSab1.1 Ensembl2141,691,912 - 42,010,301 (+)Ensembl
Crppa
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473913,813,779 - 14,114,296 (+)NCBI

Position Markers
RH128230  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0656,158,991 - 56,159,176NCBIRnor6.0
Rnor_5.0665,769,360 - 65,769,545UniSTSRnor5.0
RGSC_v3.4655,419,155 - 55,419,340UniSTSRGSC3.4
Celera652,534,095 - 52,534,280UniSTS
RH 3.4 Map6381.7UniSTS
Cytogenetic Map6q16UniSTS
AU049968  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0656,063,514 - 56,063,696NCBIRnor6.0
Rnor_5.0665,674,542 - 65,674,724UniSTSRnor5.0
RGSC_v3.4655,322,005 - 55,322,187UniSTSRGSC3.4
Cytogenetic Map6q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63626028860606186Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63760898075023446Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63810630883106308Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63819641260606431Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64167904686679046Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:664
Count of miRNA genes:270
Interacting mature miRNAs:340
Transcripts:ENSRNOT00000008312
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 3 43 57 41 19 41 8 11 74 35 36 11 8
Below cutoff 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008312   ⟹   ENSRNOP00000008312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl655,881,484 - 56,159,464 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078548   ⟹   ENSRNOP00000073650
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl655,881,387 - 56,055,489 (+)Ensembl
RefSeq Acc Id: NM_001008386   ⟹   NP_001008387
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2653,121,438 - 53,397,030 (+)NCBI
Rnor_6.0655,881,484 - 56,159,466 (+)NCBI
Rnor_5.0665,490,939 - 65,818,620 (+)NCBI
RGSC_v3.4655,139,155 - 55,419,630 (+)RGD
Celera652,259,290 - 52,534,570 (+)RGD
Sequence:
RefSeq Acc Id: XM_008764603   ⟹   XP_008762825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0655,880,136 - 55,975,240 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039112669   ⟹   XP_038968597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2653,120,264 - 53,376,637 (+)NCBI
RefSeq Acc Id: XM_039112670   ⟹   XP_038968598
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2653,120,264 - 53,397,030 (+)NCBI
RefSeq Acc Id: XR_001838196
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0655,880,141 - 56,158,251 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005505559
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2653,120,264 - 53,230,849 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001008387   ⟸   NM_001008386
- UniProtKB: Q5S6T3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762825   ⟸   XM_008764603
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000008312   ⟸   ENSRNOT00000008312
RefSeq Acc Id: ENSRNOP00000073650   ⟸   ENSRNOT00000078548
RefSeq Acc Id: XP_038968598   ⟸   XM_039112670
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968597   ⟸   XM_039112669
- Peptide Label: isoform X1
Protein Domains
ISPD_C

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13694568
Promoter ID:EPDNEW_R5088
Type:single initiation site
Name:Ispd_1
Description:isoprenoid synthase domain containing
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0655,881,383 - 55,881,443EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 65768633 65768634 G A snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 55975160 55975161 C A snv SBH/Ygl (MCW), CDS, MR/N (MCW), WKY/Gcrc (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), WKY/NCrl (RGD), WKY/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359368 AgrOrtholog
Ensembl Genes ENSRNOG00000006199 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008312 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073650 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008312 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000078548 UniProtKB/TrEMBL
Gene3D-CATH 3.90.550.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro IspD/TarI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ISPD_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ISPD_synthase_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-diphossugar_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:493574 UniProtKB/Swiss-Prot
NCBI Gene 493574 ENTREZGENE
Pfam IspD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ISPD_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Crppa PhenoGen
PROSITE ISPD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53448 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K627_RAT UniProtKB/TrEMBL
  ISPD_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5S6T4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-10 Crppa  CDP-L-ribitol pyrophosphorylase A  Ispd  isoprenoid synthase domain containing  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Ispd  isoprenoid synthase domain containing  LOC493574  notch1-induced protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC493574  notch1-induced protein      Symbol and Name status set to provisional 70820 PROVISIONAL